Is there some indicator I am missing that shows why I can't buy a certain item.

Usually its mid-late game and I am looking to upgrade or fill out any open slots, but some of the items I can afford are still grayed out.

Selling off seemingly unrelated pieces will usually let me buy the item I want, but feels like there should be a better way.

You'll need to give an example.

My guess is that you had enough gold for the recipe but you didn't have the components yet and you didn't have enough gold to buy the components and recipe at the same time.

The cost shown of the top item in a multipart item is not the rolled up cost of everything below?

Most recent item it was guardian angel. Said it was 1000 when I went to buy it and I had 1000+. But if the true cost to get there is 1000 for the guardian + all the items below I probably didn't have enough.

Thanks

Sounds about right. Guardian Angel is 2600 gold total. Recipe cost is 1200.